Re: [Useq-users] USeq installation problem w R

[Zeynep H. G. <zey...@gm...>]

Hi

It looks like in the sourcecode for ChIPSeq.java, there may be a bug that
causes the error I described in my previous email: I highlighted how this
can be changed to fix the error message with* ***:*

else {
                       String errors =
IO.runRCommandLookForError("library(DESeq)", rApplication,
resultsDirectory);
                       **** Do you mean errors != null (instead of
errors==null)? ****
                       if (errors == null || errors.length() !=0){
                               passed = false;
                               notes.append("\nError: Cannot find the
required R library.  Did you install DESeq " +
                                               "(
http://www-huber.embl.de/users/anders/DESeq/)?  See the author's websites
for installation instructions. Once installed, " +
                                               "launch an R terminal and
type 'library(DESeq)' to see if it is present. Error
message:\n\t\t"+errors+"\n\n");
                       }
               }


However, I don't know how to re-compile this within the application and make
it into the jar ChIPseq. Help would be appreciated! Thank you! - Z





On Sat, Sep 25, 2010 at 3:37 PM, Zeynep Hulya Gumus <zey...@gm...>
wrote:
> Hi
>
> I've installed USeq and also DESeq. When I open R in my local
> directory, and library(DESeq), I see that it is there.
> Now, when I try to run ChIPSeq, I get the following error:
>
> mimi@panda TEST_MIMI $ java -Xmx2G -jar ../ChIPSeq -y sam -v
> M_musculus_Jul_2007 -t ../../../MOUSE_SEQ/TRT_H3K4me/ -c
> ../../../MOUSE_SEQ/TRT_Input/ -r
> /softlib/exe/x86_64/pkg/R/2.11.1/gcc_64/bin/R -s TEST
>
> Checking parameters...
> WARNING: ignoring environment value of R_HOME
>
> The following problems were encountered when processing your parameter
> file.  Correct and restart. ->
>
> Error: Cannot find the required R library.  Did you install DESeq
> (http://www-huber.embl.de/users/anders/DESeq/)?  See the author's
> websites for installation instructions. Once installed, launch an R
> terminal and type 'library(DESeq)' to see if it is present. Error
> message:
>                null
>
> ---
> I am running it in a linux cluster, where R.11.1 is installed
> globally. However, I install the libraries locally, such that my
> .bashrc file is:
>
> # to install R:
> export R_HOME=/softlib/exe/x86_64/pkg/R/2.11.1/gcc_64
> export PATH=$R_HOME/bin${PATH+:$PATH}
> export R_LIBS=/panda_scratch_homes002/mimi/.R/mylibrary
>
> How can I make ChIPSeq correctly? Is this a problem with my paths in
> .bashrc (note that it works when I open R in the command line)?
> ChIPSeq seems to go to the global network library as opposed to
> mylibrary in my local folders.
>
> Thank you for your help!
> - Z
>